The present study analyzes the spatial distribution and seasonal distribution of live benthic foraminiferal communities in the estuary of Guadiana, the fourth largest river on the Iberian Peninsula, and establishes, through statistical analysis, their relationships with a series of environmental parameters. Forty-four superficial sediment samples were collected along distance-to-sea and elevation gradients in the winter and summer of 2010. Fiftythree foraminifera species were identified along the intertidal margins of the estuary. Foraminiferal distribution reflected seasonal variation of environmental factors, whose relative importance varied according to species tolerances. Elevation in relation to mean sea level appeared to be the most important parameter controlling foraminiferal distribution, probably because it combines the effects of a series of other variables (i.e. organic matter, sediment texture, pH and temperature). In the highest marsh areas, where environmental conditions approach survival thresholds, only some agglutinated species are able to survive. In the lower intertidal zone, where subaerial exposure is diminished and environmental conditions are generally less variable, more diverse faunas, mainly composed of calcareous species, prevail. During winter, when fluvial discharge peaks, agglutinated species represent more than 80% of the total individuals. In summer, when marine conditions prevail, calcareous species become more competitive, increase their densities and expand into higher marsh zones and estuarine upper reaches. In the estuary, three different foraminiferal assemblages are distinguished: i) Miliammina fusca assemblage, which dominates in unvegetated areas of the lower marsh and tidal flats of the mid-upper estuary; ii) Jadammina macrescens assemblage, which dominates in the highest marsh areas in the lower estuary; and iii) Ammonia aberdoveyensis assemblage, which dominates the areas of low marsh and tidal flats of the lower estuary.